User: doctor.dee005
doctor.dee005 • 20
- Reputation:
- 20
- Status:
- New User
- Location:
- Bioinformatics Center, Pune
- Last seen:
- 2 days, 6 hours ago
- Joined:
- 1 year, 9 months ago
- Email:
- d************@gmail.com
Posts by doctor.dee005
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... Where can I find gene copy numbers of each gene found in the genome?
If any way to extract information from reliable databases? ...
written 8 days ago by
doctor.dee005 • 20
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... I am using BPGA tool for pan genome analysis. It uses COG and KEGG database to find significant functional genes in genomes. The tool provide its own KEGG and COG files. I want to take updated versions.
Is there any way to do that?
**If I could get KEGG protein sequences with KO'S then also it wou ...
written 21 days ago by
doctor.dee005 • 20
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... Is there any tool or script or package to download the KEGG gene sequence in fasta format by KO ids?
I have list of KO's. ...
written 21 days ago by
doctor.dee005 • 20
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... How can I update COG and KEGG data for using it with BPGA? ...
written 22 days ago by
doctor.dee005 • 20
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... You can find the script [here][1]. Just install emboss toolkit or make sure you have fuzznuc in your path. Let me know your experience, I will improve it if needed.
This script uses given primer sets (reverse and forward) to extract the region which can be amplified.
So you can use the primers accor ...
written 5 weeks ago by
doctor.dee005 • 20
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... I have a complete genome sequence of an organism well annotated. I want to get KO ids for eanch ezymes found in the genome.
And what if I have partially annotated sequence?
Any ideas are welcomed. ...
written 6 weeks ago by
doctor.dee005 • 20
• updated
6 weeks ago by
lieven.sterck • 1.7k
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... I had downloaded greengenes, SILVA and RDP full length 16S rRNA gene databases and used universal primers of V4 regions to scan against each sequence by fuzznuc (emboss toolkit).
If required I can share my python script. ...
written 6 weeks ago by
doctor.dee005 • 20
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... I have downloaded interactions. Now I have sequences of about 4-5K proteins. I want to scan all those sequences and predict a PPI. As the webservice of stringDB does not support such large size of input, I have to do it offline.
Just simply my question is ------------ How to use PPI data to scan ag ...
written 10 months ago by
doctor.dee005 • 20
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... Web server limits the search for more sequences. I am new to this database. I wanted to predict protein-protein interactions between around 4000 protein sequences which are predicted by GenMark. ...
written 10 months ago by
doctor.dee005 • 20
• updated
10 months ago by
genomax ♦ 49k
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... Which are databases or sources for experimentally determined t cell non epitopes peptides? ...
written 16 months ago by
doctor.dee005 • 20
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